Why does the iOS keyboard have blank, black keys sometimes?
Update! This issue appears to be fixed in iOS 10. Hooray!
This is an iOS 9 bug that affects the dark system keyboard. Some of the keys appear blank after a full-screen pop-over (like Touch ID) is dismissed.
We have already reported this issue to Apple and are hopeful that it will be addressed in a future update.
For the time being you can restore the normal keyboard appearance by switching to any other keyboard (e.g. emoji) and then back again.